Structural Insights into the Catalytic Mechanism of Escherichia coli Selenophosphate Synthetase

Abstract

Selenophosphate synthetase (SPS) catalyzes the synthesis of selenophosphate, the selenium donor for the biosynthesis of selenocysteine and 2-selenouridine residues in seleno-tRNA. Selenocysteine, known as the 21st amino acid, is then incorporated into proteins during translation to form selenoproteins which serve a variety of cellular processes. SPS activity is dependent on both Mg 2؉ and K ؉ and uses ATP, selenide, and water to catalyze the formation of AMP, orthophosphate, and selenophosphate. In this reaction, the gamma phosphate of ATP is transferred to the selenide to form selenophosphate, while ADP is hydrolyzed to form orthophosphate and AMP. Most of what is known about the function of SPS has derived from studies investigating Escherichia coli SPS (EcSPS) as a model system. Here we report the crystal structure of the C17S mutant of SPS from E. coli (EcSPS C17S ) in apo form (without ATP bound). EcSPS C17S crystallizes as a homodimer, which was further characterized by analytical ultracentrifugation experiments. The glycine-rich N-terminal region (residues 1 through 47) was found in the open conformation and was mostly ordered in both structures, with a magnesium cofactor bound at the active site of each monomer involving conserved aspartate residues. Mutating these conserved residues (D51, D68, D91, and D227) along with N87, also found at the active site, to alanine completely abolished AMP production in our activity assays, highlighting their essential role for catalysis in EcSPS. Based on the structural and biochemical analysis of EcSPS reported here and using information obtained from similar studies done with SPS orthologs from Aquifex aeolicus and humans, we propose a catalytic mechanism for EcSPS-mediated selenophosphate synthesis. Selenium is an essential nutrient that has been linked to many human diseases (27) related to hormone regulation (35, 38), immune response (16, 42), protection from reactive oxygen species (12), and brain function (4). Deficiencies in selenium intake have been implicated in several health disorders over the past two decades, including cancer (5), cardiovascular disease (3), male infertility (43), asthma (39), and viral infections (29). Seleniumcontaining proteins, or selenoproteins, are expressed in many organisms and tissues (26,34,40). Studies have shown that mutations in some of these selenoproteins can lead to decreased activity resulting in abnormal hormone metabolism (8, 9) and rigid-spine muscular dystrophy (30).Selenium has been shown to be incorporated into enzymes/ proteins either as a selenocysteine (7), which occurs at a specific position in the protein sequence and participates in the protein's catalytic action, or as a selenomethionine, which results from random substitution of selenium in place of sulfur in methionine and exerts no effect on the enzymatic activity of the protein (15). Incorporation of selenocysteine, commonly referred to as the 21st amino acid, is mediated by a UGA codon-directed cotranslation involving four genes, selA, selB, selC, and se...

Formation of a Ternary Complex for Selenocysteine Biosynthesis in Bacteria

“…Therefore, homodecamerization, and consequently, the Ser-Sec conversion and selenoprotein biosynthesis, is dependent on the N-terminal region (or N terminus), as we observed by functional complementation with the N-terminally truncated E. coli SelA. Similar results from A. aeolicus SelA N-terminal mutants (27) (7,10), to form Sec-tRNA Sec . The SPS dimerization interface is composed of the ␤-sheet domain of each monomer, a common structural characteristic of the PurM protein superfamily (7).…”

“…We suggest that this conformational change corresponds to the region from Glu 159 to Val 161 (␣-helix 4) of E. coli SPS. Although no information about H/D exchange was obtained for this ␣-helix, analysis of the E. coli SPS crystal structure (7) indicates that it is in the middle of the linker between the aminoimidazole ribonucleotide synthetase (AIRS)-related and C-terminal domains, which is consistent with the SelA-tRNA Sec -SPS interaction. Regions close to the active sites of SPS were observed to be hidden from H/D exchange, and we conclude that these regions may be the interaction points that enable the formation of the ternary complex.…”

“…In addition, consistent with the SPS crystallographic structures (PDB ID 3U0O) that were previously described, the glycine-rich N-terminal region of SPS was observed to be flexible in solution, showing high levels of deuterium exchange even after low deuterium exposure time. This flexibility allows the formation of the SPS active site on its "closed" form, upon ATP binding, releasing the catalysis product in its "open" form (7,10).…”

“…A flexible conformation of SPS is certainly required to facilitate its interaction with the SelA-tRNA Sec complex, as observed for the NifS-like-SPS interaction (7,12). In fact, the glycine-rich N-terminal region of SPS is hidden from the solvent after SelA-tRNA Sec -SPS formation, as observed by H/DEx-MS, and SPS with an N-terminal truncation does not interact with SelA-tRNA Sec , as shown by fluorescence anisotropy spectroscopy experiments.…”

“…It is possible that thioredoxin reductase, which is involved in selenite reduction, is also involved in delivering selenide for SPS (3,13). After selenophosphate is synthesized, it remains bound to the active-site cavity of SPS until ADP hydrolysis occurs and the product release is completed (7,10).…”